Meeting Abstract
We sequenced the genome of the intertidal, herbivorous fish, Cebidichthys violaceus (Teleostei: Stichaeidae) to elucidate the genetic underpinnings of dietary specialization and intertidal existence in this species. C. violaceus is part of a phylogeny that showed independent intertidal invasion and evolution of herbivory in comparison to other herbivorous stichaeids (e.g., Xiphister mucosus). A juvenile individual collected from San Simeon, California was used to sequence the C. violaceus genome, and the genome was generated with Illumina and Pacific Biosciences (PacBio) datasets with 107X and 37X coverage, respectively. From our genomic datasets, we conducted a de novo assembly of the Illumina reads and then a hybrid assembly with both Illumina and PacBio datasets. We estimated the genome to be 526,436,767 base pairs with a N50 contig size of 6.7 Mb. In conjunction, we generated RNA-Seq data from nine tissue types (brain, gill, gonads, heart, liver, mid intestine, proximal intestine, pyloric caeca, and spleen) for annotation of the genome. We are using our transcriptomic data sets to better understand the multitude of processes that allow a fish to be herbivorous and to tolerate the vagaries of intertidal existence (e.g., temperature fluxes, and breathing water and air). Moreover, what we learn from C. violaceus will be used to inform analyses of other fishes in the family Stichaeidae, which features dietary diversity, ontogenetic dietary shifts (including a shift from carnivory to herbivory in C. violaceus and other taxa), and large biogeographic ranges spanning the eastern and western Pacific Ocean.
